Nov. 22

Install packages from

  • Bioconductor ?
    1. First install BiocManager from CRAN
    2. Run the R command BiocManager::install("package_name")
  • GitHub ?
    1. Install devtools
    2. Run the R command devtools::install_github("username/repository").
  • Source code ?
    1. Put the source.tar.gz in your working directory…
    2. Run the R command install.package("source.tar.gz", repos = NULL, type = "source").

Exercises

Install limma

limma is the favorite package of anyone that wants to analyze gene expression data (microarray, RNA-seq, NanoString etc.)

Install it with the command:

BiocManager::install("limma")

Explore the package

  1. Load : library(limma)
  2. Look at the main help page
?`limma-package`
  1. Look at the first vignette : vignette("intro", package = "limma")

Install the “ReMUSE” course’s package

The course’s material is in fact an R package. Install it from GitHub with the command:

devtools::install_github("vguillemot/ReMUSE")